Thanks to the creator Matt140, we now have a program that succesfully converts to and from the .duc format.
A link to his post:
http://projectpokemon.org/forums/showthread.php?p=44306#post44306
Oh and by the way the AR I have is for the DSi and is sold at Toys R Us for $20. In other words, it is the first product that reads and writes saves, that you DON'T have to buy over the internet.

I tried AR max for the source file, then converted it to every .sav that shunny allows.
None of shunny's saves are working.
---------- Post added at 06:53 AM ---------- Previous post was at 06:50 AM ----------
This Action Replay I have is not ar max. Maybe that's the problem.

About an hour ago I bought a newer Action Replay. This one has a micro sd card slot and allows you to backup and restore save files to the micro sd card.
The problem is though the file is a .duc not a .sav so pokesav won't open it. Does anyone know how to convert it?
Oh, and by the way it can run home brew.

I've heard that if a save file was originally protected, like Colosseum and it can't be restored to a different memory card than the one it was backed up from due to the fact that each memory card has a unique serial number that is used to encrypt protected saves.

I'm very sorry everyone, I am no longer allowed to trade Pokemon over Wi-Fi. My parents both think it is "wrong" to generate Pokemon and trade them. Please do not PM me about my trading thread, as I will not be checking or updating it any longer. You may PM though, to battle, voice chat, or do other things among Wi-Fi.
I am sorry for any inconvenience this causes.

Hello all, I can trade shiny Pokemon and event Pokemon. You may ask for customized natures. The IVs of every shiny I trade will be as high as possible (usually between 25 and 31, 31 is max). I am on Wi-Fi every Saturday.
All Pokemon I trade pass the latest version of the Pokemon Legality checker, and are exactly the same as if obtained in game, meaning THEY ARE OFFICIAL NINTENDO TOURNAMENT SAFE.
I will have all requests ready to trade in less than one week.

Hello all, I can trade shiny Pokemon and event Pokemon. You may ask for customized natures. The IVs of every shiny I trade will be as high as possible (usually between 25 and 31, 31 is max). I am on Wi-Fi every Saturday.
All Pokemon I trade pass the latest version of the Pokemon Legality checker, and are exactly the same as if obtained in game, meaning THEY ARE OFFICIAL NINTENDO TOURNAMENT SAFE.
I will have all requests ready to trade in less than one week.
Here is my thread: http://projectpokemon.org/forums/showthread.php?t=3655&page=12